D J Lipman

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Domain enhanced lookup time accelerated BLAST
    Grzegorz M Boratyn
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Biol Direct 7:12. 2012
  2. pmc Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses
    Edward C Holmes
    Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
    PLoS Biol 3:e300. 2005
  3. pmc Splign: algorithms for computing spliced alignments with identification of paralogs
    Yuri Kapustin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20814, USA
    Biol Direct 3:20. 2008
  4. pmc Differences in evolutionary pressure acting within highly conserved ortholog groups
    Teresa M Przytycka
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Evol Biol 8:208. 2008
  5. pmc Making (anti)sense of non-coding sequence conservation
    D J Lipman
    National Center for Biotechnology Information, National Library of Medicine, NIH, Building 38A 8N803, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 25:3580-3. 1997
  6. pmc The relationship of protein conservation and sequence length
    David J Lipman
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Evol Biol 2:20. 2002
  7. pmc GenBank
    Dennis A Benson
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 38:D46-51. 2010
  8. pmc Database resources of the National Center for Biotechnology Information
    David L Wheeler
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 36:D13-21. 2008
  9. pmc GenBank
    D A Benson
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 25:1-6. 1997
  10. pmc GenBank
    D A Benson
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 26:1-7. 1998

Collaborators

Detail Information

Publications37

  1. pmc Domain enhanced lookup time accelerated BLAST
    Grzegorz M Boratyn
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Biol Direct 7:12. 2012
    ....
  2. pmc Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses
    Edward C Holmes
    Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
    PLoS Biol 3:e300. 2005
    ....
  3. pmc Splign: algorithms for computing spliced alignments with identification of paralogs
    Yuri Kapustin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20814, USA
    Biol Direct 3:20. 2008
    ..Several factors such as presence of paralogs, small exons, non-consensus splice signals, sequencing errors and polymorphic sites pose recognized difficulties to existing spliced alignment algorithms...
  4. pmc Differences in evolutionary pressure acting within highly conserved ortholog groups
    Teresa M Przytycka
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Evol Biol 8:208. 2008
    ..g. Proteobacteria or Firmicutes)...
  5. pmc Making (anti)sense of non-coding sequence conservation
    D J Lipman
    National Center for Biotechnology Information, National Library of Medicine, NIH, Building 38A 8N803, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 25:3580-3. 1997
    ..The formation of such duplexes may be essential for recognition by post-transcriptional regulatory systems. The conservation may then be explained by selection against the dominant negative effect of allelic divergence...
  6. pmc The relationship of protein conservation and sequence length
    David J Lipman
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Evol Biol 2:20. 2002
    ..However, additional evolutionary forces that affect the length of a protein may be revealed by studying the length distributions of proteins evolving under weaker functional constraints...
  7. pmc GenBank
    Dennis A Benson
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 38:D46-51. 2010
    ..Complete bi-monthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI homepage: www.ncbi.nlm.nih.gov...
  8. pmc Database resources of the National Center for Biotechnology Information
    David L Wheeler
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 36:D13-21. 2008
    ..Augmenting the web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov...
  9. pmc GenBank
    D A Benson
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 25:1-6. 1997
    ..All of NCBI's services are offered through the World Wide Web. In addition, there are specialized server/client versions as well as FTP and e-mail server access...
  10. pmc GenBank
    D A Benson
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 26:1-7. 1998
    ..In addition to FTP, e-mail and server/client versions of Entrez and BLAST, NCBI offers a wide range of World Wide Web retrieval and analysis services of interest to biologists...
  11. pmc GenBank
    Dennis A Benson
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 31:23-7. 2003
    ..Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI home page at: http://www.ncbi.nlm.nih.gov...
  12. pmc GenBank: update
    Dennis A Benson
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 32:D23-6. 2004
    ..Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI home page at: http://www.ncbi.nlm.nih.gov...
  13. pmc GenBank
    D A Benson
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 28:15-8. 2000
    ..NCBI also offers a wide range of WWW retrieval and analysis services based on GenBank data. The GenBank database and related resources are freely accessible via the NCBI home page at http://www.ncbi.nlm.nih.gov..
  14. pmc CDART: protein homology by domain architecture
    Lewis Y Geer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Genome Res 12:1619-23. 2002
    ..Searches can be further refined by taxonomy and by selecting domains of interest. CDART is available at http://www.ncbi.nlm.nih.gov/Structure/lexington/lexington.cgi...
  15. pmc GenBank
    Dennis A Benson
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 35:D21-5. 2007
    ..Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage (www.ncbi.nlm.nih.gov)...
  16. pmc GenBank
    Dennis A Benson
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 36:D25-30. 2008
    ..Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov...
  17. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 37:D5-15. 2009
    ..Augmenting many of the web applications is custom implementation of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov...
  18. pmc GenBank
    Dennis A Benson
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Nucleic Acids Res 37:D26-31. 2009
    ..Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov...
  19. pmc The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages
    Yuri I Wolf
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Proc Natl Acad Sci U S A 106:7273-80. 2009
    ..Thus, genome evolution fits a simple model with approximately uniform rates of gene gain and loss, without major bursts of genomic innovation...
  20. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 38:D5-16. 2010
    ..Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov...
  21. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 39:D38-51. 2011
    ..Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov...
  22. pmc Database resources of the National Center for Biotechnology Information
    David L Wheeler
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 35:D5-12. 2007
    ..Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov...
  23. pmc GenBank
    Dennis A Benson
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 34:D16-20. 2006
    ..Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI Homepage at www.ncbi.nlm.nih.gov...
  24. pmc Patterns in interspecies similarity correlate with nucleotide composition in mammalian 3'UTRs
    Svetlana A Shabalina
    National Center for Biotechnology Information, National Institutes of Health, 8600 Rockville Pike, Building 38A, Bethesda, MD 20894, USA
    Nucleic Acids Res 31:5433-9. 2003
    ..Our results provide evidence on the importance of moderately conserved regions in 3'UTRs and suggest that regulatory functions of 3'UTRs might utilize gene-specific information in these regions...
  25. pmc Database resources of the National Center for Biotechnology Information
    David L Wheeler
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 33:D39-45. 2005
    ..Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of the resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov...
  26. pmc GenBank
    Dennis A Benson
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 30:17-20. 2002
    ..NCBI also offers a wide range of World Wide Web retrieval and analysis services based on GenBank data. The GenBank database and related resources are freely accessible via the NCBI home page at http://www.ncbi.nlm.nih.gov...
  27. pmc Database resources of the National Center for Biotechnology Information
    David L Wheeler
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 34:D173-80. 2006
    ..Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov...
  28. pmc Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    S F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 25:3389-402. 1997
    ..PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily...
  29. pmc Extracting protein alignment models from the sequence database
    A F Neuwald
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 25:1665-77. 1997
    ..Moreover, this method automatically generates models of these ancient conserved regions for rapid and sensitive screening of sequences...
  30. pmc Relative contributions of intrinsic structural-functional constraints and translation rate to the evolution of protein-coding genes
    Yuri I Wolf
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
    Genome Biol Evol 2:190-9. 2010
    ..Together the intrinsic constraints and translation rate account for approximately 50% of the variance of the ERs. The contribution of constraints is estimated to be 3- to 5-fold greater than the contribution of translation rate...
  31. pmc Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals
    Svetlana A Shabalina
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 32:1774-82. 2004
    ....
  32. pmc GenBank
    D A Benson
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 27:12-7. 1999
    ..The GenBank database and related resources are freely accessible via the URL: http://www.ncbi.nlm.nih.gov..
  33. pmc GenBank
    Dennis A Benson
    Department of Health and Human Services, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 33:D34-8. 2005
    ..Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI Homepage at http://www.ncbi.nlm.nih.gov...
  34. pmc Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage
    Yang Huang
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 37:6799-810. 2009
    ..Collectively, the results fit the concept of selection against mistranslation-induced protein misfolding being one of the factors shaping the evolution of both coding and non-coding sequences...
  35. ncbi request reprint Comment on "Large-scale sequence analysis of avian influenza isolates"
    Edward C Holmes
    Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA
    Science 313:1573; author reply 1573. 2006
    ..However, we show that this observation is likely to be an artifact related to the location of PB1-F2 in the +1 reading frame of the PB1 gene...
  36. ncbi request reprint Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution
    Elodie Ghedin
    The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, Maryland 20850, USA
    Nature 437:1162-6. 2005
    ..All data from this project are being deposited, without delay, in public archives...
  37. pmc Stochastic processes are key determinants of short-term evolution in influenza a virus
    Martha I Nelson
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
    PLoS Pathog 2:e125. 2006
    ..Thus, predicting future patterns of influenza virus evolution for vaccine strain selection is inherently complex and requires intensive surveillance, whole-genome sequencing, and phenotypic analysis...